On Tue, Jan 15, 2013, Thomas Exner wrote:
>
> I would like to run TI calculations on a set of slightly modified
> ligands. The parameters are generated by antechamber (partial charges
> are calculated with Gaussian) and I renamed common atom to match in
> each ligand. But unfortunately, antechamber generates different atom
> orderings in each parameter file and, thus, they are also in different
> order in the amber input files. Is there a way to reorder the atoms that
> they are consistently ordered in all input files as required for sander.
> To be consistent with earlier simulations I still use AMBER10 for the
> calculations.
Are you using a prepi format in antechamber? If so, don't; use mol2 instead.
I think(!?!) antechamber will preserve the atom order for formats other than
prepi. Not sure, though.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 15 2013 - 05:30:06 PST
